Analysis of biogeographic ancestry reveals complex genetic histories for indigenous communities of St. Vincent and Trinidad

Abstract

Objectives: From a genetic perspective, relatively little is known about how mass emigrations of African, European, and Asian peoples beginning in the 16th century affected Indigenous Caribbean populations. Therefore, we explored the impact of serial colonization on the genetic variation of the first Caribbean islanders.

Materials and methods: Sixty-four members of St. Vincent's Garifuna Community and 36 members of Trinidad's Santa Rosa First People's Community (FPC) of Arima were characterized for mitochondrial DNA and Y-chromosome diversity via direct sequencing and targeted SNP and STR genotyping. A subset of 32 Garifuna and 18 FPC participants were genotyped using the GenoChip 2.0 microarray. The resulting data were used to examine genetic diversity, admixture, and sex biased gene flow in the study communities.

Results: The Garifuna were most genetically comparable to African descendant populations, whereas the FPC were more similar to admixed American groups. Both communities also exhibited moderate frequencies of Indigenous American matrilines and patrilines. Autosomal SNP analysis indicated modest Indigenous American ancestry in these populations, while both showed varying degrees of African, European, South Asian, and East Asian ancestry, with patterns of sex-biased gene flow differing between the island communities.

Discussion: These patterns of genetic variation are consistent with historical records of migration, forced, or voluntary, and suggest that different migration events shaped the genetic make-up of each island community. This genomic study is the highest resolution analysis yet conducted with these communities, and provides a fuller understanding of the complex bio-histories of Indigenous Caribbean peoples in the Lesser Antilles.

Keywords: Caribbean; Y-chromosome; admixture; autosomal DNA; mtDNA.

FIGURE 1

Maps of Caribbean islands and sampled communities. (a) A map of the Caribbean basin; (b) a map of the study islands in the Lesser Antilles; (c) a map showing the sampling locales in St. Vincent and Trinidad (Indigenous names for the study islands are in parentheses, adapted from Sued-Badillo 2003.)

FIGURE 2

PCA plots of comparative and study populations. (a) PC1 versus PC2, explaining 76.5% of the variation; (b) PC 3 versus PC 4, explaining 16.2% of the variation. A list of the comparative populations may be found in Table S6. PCA, principal components analysis

FIGURE 3

Admixture plots of comparative and Indigenous Caribbean populations, K = 5

FIGURE 4

Mean and median global ancestry estimates for Indigenous Caribbean and comparative populations

FIGURE 5

Sex bias plots of proportional ancestry for (a) African (AFR), (b) Indigenous American (AMR), (c) East Asian (EAS), (d) European (EUR), and (e) South Asian ancestry in Indigenous Caribbean communities. Trinidad First People’s Community is shown in red and the Vincentian Garifuna in blue